PDB-3vfh: BlaC E166A CDC-1 Acyl-Intermediate

ID or keywords:

Entry

Database: PDB / ID: 3vfh

Title

BlaC E166A CDC-1 Acyl-Intermediate

Components

Beta-lactamase

Keywords

Hydrolase/Hydrolase Inhibitor / beta-lactamase / serine hydrolase / serine esterase / acyl-intermediate / Hydrolase-Hydrolase Inhibitor complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.57 Å

Authors

Mire, J.A. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: BlaC-Specific Fluorogenic Probes for Rapid Tuberculosis Detection
Authors: Xie, H. / Mire, J.A. / Kong, Y. / Chang, M. / Sacchettini, J.C. / Cirillo, J.D. / Rao, J.

History

Deposition	Jan 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3vfh.cif.gz	410.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3vfh.ent.gz	337.6 KB	Display	PDB format
PDBx/mmJSON format	3vfh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3vfh_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3vfh_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3vfh_validation.xml.gz	42.3 KB	Display
Data in CIF	3vfh_validation.cif.gz	56.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfh ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfh	HTTPS FTP

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Related structure data

Related structure data	3vffC 2gdnS 4ebi PDB Unreleased entry 4ebl 4ebm PDB Unreleased entry 4ebn 4ebo PDB Unreleased entry 4ebp C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3zhh-1 6b5x-2 4ebl-2 4ebn-3 4jlf-d 6b6b-d 6b5y-2 5nj2-2 3zhh-4 3n7w-d 3ndg-d 6d18-d 3vff-4 7d5j-1 1ymx-2 3nde-d 4ebn-1 4dds-2 7k2x-8 6b5x-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: TB-Rv2068c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (5) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

123 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

hetero molecules

defined by author&software
30.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase

hetero molecules

defined by author&software
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Beta-lactamase

hetero molecules

defined by author&software
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Beta-lactamase

hetero molecules

defined by author&software
30.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.396, 97.459, 110.958
Angle α, β, γ (deg.)	90.00, 108.37, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase / Penicillinase Mass: 30489.074 Da / Num. of mol.: 4 / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CD6 / (2R)-5-methylidene-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid Mass: 332.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₁₆N₂O₄S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.18 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 120 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97929 Å

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97929 Å / Relative weight: 1

Reflection

Resolution: 2.57→50 Å / Num. all: 51168 / Num. obs: 49807 / % possible obs: 99 % / Observed criterion σ(I): 2.17 / Redundancy: 4 % / B_iso Wilson estimate: 45.82 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 12

Reflection shell

Resolution (Å)	Num. unique all	Diffraction-ID	% possible all
2.57-2.64	2491	1	98.8
2.64-2.69	2448	1	98.5
2.69-2.74	2505	1	98.7
2.74-2.8	2464	1	98.7
2.8-2.86	2450	1	98.5
2.86-2.93	2492	1	99
2.93-3	2445	1	98.9
3-3.08	2507	1	98.9
3.08-3.17	2504	1	99.5
3.17-3.28	2481	1	99.3
3.28-3.39	2516	1	99.6
3.39-3.53	2483	1	99.6
3.53-3.69	2494	1	99.6
3.69-3.88	2517	1	99.7
3.88-4.13	2524	1	99.7
4.13-4.45	2521	1	99.4
4.45-4.89	2486	1	99.1
4.89-5.6	2523	1	99.3
5.06-7.05	2530	1	98.9
7.05-50	2497	1	96.1

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2GDN

2gdn

Resolution: 2.57→47.087 Å / SU ML: 0.7 / σ(F): 0 / σ(I): 0 / Phase error: 27.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2519	2523	5.07 %	random 5.07%
R_work	0.2254	-	-	-
obs	0.2268	49807	97.36 %	-
all	-	51168	-	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.903 Å² / k_sol: 0.349 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.8112 Å²	-0 Å²	-5.2826 Å²
2-	-	-7.3641 Å²	0 Å²
3-	-	-	1.553 Å²

Refinement step

Cycle: LAST / Resolution: 2.57→47.087 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7928	0	81	114	8123

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8162
X-RAY DIFFRACTION	f_angle_d	1.176	11150
X-RAY DIFFRACTION	f_dihedral_angle_d	14.665	2928
X-RAY DIFFRACTION	f_chiral_restr	0.067	1280
X-RAY DIFFRACTION	f_plane_restr	0.007	1470

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.57-2.621	0.4048	86	0.3338	1918	X-RAY DIFFRACTION	71
2.621-2.6745	0.3677	129	0.329	2645	X-RAY DIFFRACTION	98
2.6745-2.7326	0.3103	121	0.3168	2685	X-RAY DIFFRACTION	98
2.7326-2.7962	0.3406	128	0.308	2632	X-RAY DIFFRACTION	99
2.7962-2.8661	0.3334	150	0.2947	2637	X-RAY DIFFRACTION	99
2.8661-2.9436	0.324	157	0.2849	2646	X-RAY DIFFRACTION	99
2.9436-3.0302	0.322	124	0.2726	2628	X-RAY DIFFRACTION	99
3.0302-3.128	0.3118	134	0.2673	2689	X-RAY DIFFRACTION	99
3.128-3.2397	0.2612	172	0.2557	2640	X-RAY DIFFRACTION	99
3.2397-3.3694	0.2874	149	0.2503	2702	X-RAY DIFFRACTION	100
3.3694-3.5227	0.2338	155	0.2247	2654	X-RAY DIFFRACTION	100
3.5227-3.7084	0.2454	127	0.2122	2703	X-RAY DIFFRACTION	100
3.7084-3.9406	0.2379	150	0.2041	2692	X-RAY DIFFRACTION	100
3.9406-4.2447	0.2122	129	0.1899	2699	X-RAY DIFFRACTION	100
4.2447-4.6715	0.1981	146	0.1703	2687	X-RAY DIFFRACTION	99
4.6715-5.3467	0.1955	160	0.1783	2661	X-RAY DIFFRACTION	99
5.3467-6.7331	0.248	161	0.2261	2689	X-RAY DIFFRACTION	99
6.7331-47.0949	0.2314	145	0.2039	2677	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.2903	-0.4648	1.6408	3.2078	0.2801	3.0264	0.4375	0.2208	-0.671	-0.7346	-0.1268	-0.0278	0.67	0.0261	-0.2702	0.3591	-0.0386	-0.0012	0.2749	0.0137	0.1535	27.7173	-0.9591	-5.8375
2	2.2133	0.751	0.952	2.213	0.792	2.5578	-0.1976	-0.0681	0.6183	0.152	0.0539	0.0402	-0.2901	0.3486	0.1454	0.331	-0.053	0.0284	0.2235	0.0168	0.2688	34.1481	17.9918	14.0077
3	2.4119	1.3788	2.2313	5.2041	2.0428	4.4397	-0.44	-0.4746	1.4917	-0.058	-0.2904	0.6564	-0.6053	-0.439	0.0944	0.4799	0.063	-0.044	0.5161	-0.0859	0.4239	23.3039	22.2778	23.3064
4	1.3713	0.271	0.3479	1.4366	0.8468	1.0925	-0.1455	0.0538	0.2085	0.0189	0.1049	-0.0198	-0.2714	0.1056	0.0459	0.2266	-0.0269	0.0201	0.2081	0.0344	0.1353	33.6091	12.8223	10.3218
5	1.4971	-0.5915	1.3289	3.5302	-1.204	2.4464	-0.11	0.0683	-0.0122	0.2455	0.1038	0.1119	-0.4145	-0.0683	0.1003	0.1685	-0.0356	0.006	0.2152	0.0281	0.1341	25.3312	3.6751	3.6486
6	1.0162	0.329	1.0081	1.0116	-0.4623	2.8218	-0.0941	-0.0793	0.1701	0.123	0.1246	0.1726	-0.157	-0.1001	0.076	0.1831	0.0443	-0.0174	0.1037	-0.0377	0.2439	6.703	8.0491	27.996
7	0.6824	-0.449	-0.0759	3.5189	-0.6229	2.1681	-0.0376	-0.0496	0.2317	-0.1522	0.2286	0.1898	-0.415	-0.026	-0.1771	0.2058	0.0204	0.0828	0.1764	-0.0754	0.3263	0.0514	10.5991	31.2243
8	1.0599	-0.1094	1.1215	1.5554	-0.4252	2.3139	-0.0691	-0.0634	0.0248	-0.1309	0.0261	0.0192	-0.1914	0.0852	0.0298	0.1691	0.0041	0.0388	0.1464	-0.0414	0.1792	11.2507	-1.3295	35.3826
9	5.2417	-2.0519	2.1636	1.8751	-1.4987	2.8237	0.0385	0.0832	0.2276	-0.2039	-0.1108	-0.1922	-0.0588	0.0549	0.1095	0.2975	0.038	0.0171	0.2344	-0.0443	0.2396	26.8967	-21.3316	-3.0534
10	3.3091	-0.002	0.1386	0.8655	-0.9368	1.9582	0.1491	-0.408	-0.5897	0.0075	0.4022	0.6113	0.3793	-0.4364	-0.2026	0.2629	-0.0237	-0.0153	0.2562	0.1423	0.4849	8.3402	-35.2985	14.6325
11	2.4881	-0.6974	-0.3881	2.9513	-0.9351	2.5729	0.1965	-0.3408	-0.314	-0.065	0.1979	-0.4966	0.5317	0.504	-0.4499	0.2597	0.0969	-0.2515	0.0844	-0.0437	0.4535	13.3618	-41.5674	3.3712
12	2.8856	0.1402	-0.0542	2.0352	-0.5297	1.5067	-0.0785	-0.0317	-0.1231	0.0317	0.1694	0.1956	0.2529	0.04	-0.0954	0.1342	0.0296	-0.0141	0.0862	-0.0165	0.1118	16.1718	-23.2476	6.161
13	5.6688	1.6789	2.02	2.2574	-0.6799	2.6188	0.0688	-0.2611	0.8038	0.5369	-0.012	0.5761	-0.6249	-0.3669	-0.1809	0.3561	0.0911	0.1881	0.2766	0.0696	0.2686	8.8905	-22.2856	49.8039
14	1.5043	-0.6308	0.6295	1.5508	0.0983	1.4972	0.0538	0.0782	-0.1627	0.0451	0.1419	-0.3251	0.3293	0.2327	-0.0332	0.5177	0.0269	0.0101	0.1626	0.1694	-0.0191	24.8767	-36.2908	43.4661
15	2.4936	-0.6064	1.3265	3.2525	1.3868	1.6461	0.5325	0.6342	-0.5629	-0.4869	-0.4166	0.299	0.6224	0.0965	-0.2866	0.662	0.1448	-0.0639	0.4296	-0.0457	0.247	25.2653	-44.6038	27.1776
16	1.2061	-0.8103	0.612	1.5696	-0.1361	0.6059	-0.0783	-0.1576	-0.0973	0.1282	0.105	0.0845	0.1911	-0.0323	0.0247	0.3122	-0.0122	0.0344	0.213	0.0448	0.1237	23.2018	-35.33	42.0002
17	2.4971	0.3345	0.5417	2.8151	-0.893	1.2081	-0.2254	-0.0385	-0.2707	-0.3248	0.3026	0.2625	0.1177	-0.236	-0.0534	0.2134	-0.0188	0.0407	0.2086	0.0647	0.1399	12.1388	-26.7637	42.0744

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 29:60)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 61:102)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 103:118)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 119:229)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 230:293)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 29:144)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 145:212)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 213:293)
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESSEQ 29:57)
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESSEQ 58:144)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 145:179)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 180:293)
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESSEQ 29:57)
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESSEQ 58:92)
15	X-RAY DIFFRACTION	15	CHAIN D AND (RESSEQ 93:131)
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESSEQ 132:238)
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESSEQ 240:293)

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